ZNF410 zinc finger protein 410 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZNF410provided by HGNC
Official Full Name: zinc finger protein 410provided by HGNC
Primary source: HGNC:HGNC:20144
See related: Ensembl:ENSG00000119725 MIM:619427; AllianceGenome:HGNC:20144
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: APA1; APA-1
Summary: Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis (RPKM 23.4), bone marrow (RPKM 18.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q24.3

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (73886859..73932521)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (68094511..68140172)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (74353562..74399224)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ZNF410 represses fetal globin by singular control of CHD4.
Title: ZNF410 represses fetal globin by singular control of CHD4.
ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression.
Title: ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression.
The HG-stimulated proliferative capacity was abolished upon decreasing O-GlcNAcylation, which could be reversed gradually by the simultaneous overexpression of APA1 and GJC1. Therefore, GJC1 could be a potential target for preventing liver cancer in patients with diabetes.
Title: High glucose stimulates proliferative capacity of liver cancer cells possibly via O-GlcNAcylation-dependent transcriptional regulation of GJC1.
No association was found between Apa1 genotypes and osteoporosis
Title: [Apa1 VDR polymorphism and osteoporosis risk in postmenopausal Mexican women].
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
VDR polymorphism genotypes and haplotypes did not directly alter recurrence risk, but the reduction in risk associated with high dairy product intake was confined to individuals with ApaI aA/AA genotype.
Title: Dairy products, polymorphisms in the vitamin D receptor gene and colorectal adenoma recurrence.
APA1 has a role in inducing extracellular matrix remodeling genes
Title: Induction of extracellular matrix-remodeling genes by the senescence-associated protein APA-1.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

D14S1179 (e-PCR)
- UniSTS:154641

G20802 (e-PCR)
- UniSTS:35892

A006H11 (e-PCR)
- UniSTS:35893

D14S705E (e-PCR)
- UniSTS:50054

A002U02 (e-PCR)
- UniSTS:74701

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: zinc finger protein 410

Names: another partner for ARF 1; clones 23667 and 23775 zinc finger protein; zinc finger protein APA-1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001242924.2 → NP_001229853.1 zinc finger protein 410 isoform a

See identical proteins and their annotated locations for NP_001229853.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a)

Source sequence(s)

AA652386, AC005480, AC005520, AK293350

Consensus CDS

CCDS55929.1

UniProtKB/TrEMBL

B2RCP6, Q53FM1

Related

ENSP00000407130.3, ENST00000442160.7

Conserved Domains (4) summary

sd00017
Location:298 → 320

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:271 → 290

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:342 → 367

zf-H2C2_2; Zinc-finger double domain

pfam15909
Location:268 → 351

zf-C2H2_8; C2H2-type zinc ribbon
NM_001242926.2 → NP_001229855.1 zinc finger protein 410 isoform c

See identical proteins and their annotated locations for NP_001229855.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in both the 5' and central coding regions, and it also lacks an exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (c) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AA652386, AC005480, BC050683

Consensus CDS

CCDS55930.1

UniProtKB/TrEMBL

B2RCP6, Q53FM1

Related

ENSP00000323293.6, ENST00000324593.10

Conserved Domains (3) summary

COG5048
Location:148 → 367

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:281 → 303

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:254 → 273

ZF_C2H2; C2H2 Zn finger [structural motif]
NM_001242927.2 → NP_001229856.1 zinc finger protein 410 isoform d

See identical proteins and their annotated locations for NP_001229856.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks two alternate in-frame exons in the 5' coding region, and it also lacks an exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (d) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AA652386, AC005480, AK299138

Consensus CDS

CCDS55931.1

UniProtKB/TrEMBL

B4DPE9

Related

ENSP00000442228.1, ENST00000540593.5

Conserved Domains (4) summary

sd00017
Location:208 → 230

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:181 → 200

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:252 → 277

zf-H2C2_2; Zinc-finger double domain

pfam15909
Location:178 → 261

zf-C2H2_8; C2H2-type zinc ribbon
NM_001242928.2 → NP_001229857.1 zinc finger protein 410 isoform e

See identical proteins and their annotated locations for NP_001229857.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in its 5' UTR and 5' coding region, uses an alternate downstream start codon, and includes alternate exon structure in the 3' coding region, compared to variant 1. The encoded isoform (e) has distinct N- and C-termini and is shorter than isoform a.

Source sequence(s)

AA652386, AC005480, BC000330, DC379519

Conserved Domains (4) summary

sd00017
Location:85 → 107

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:58 → 77

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:129 → 154

zf-H2C2_2; Zinc-finger double domain

pfam13900
Location:276 → 310

GVQW; Putative domain of unknown function
NM_021188.3 → NP_067011.1 zinc finger protein 410 isoform b

See identical proteins and their annotated locations for NP_067011.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, and it also lacks an exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AA652386, AC005480, AK223261

Consensus CDS

CCDS9821.1

UniProtKB/Swiss-Prot

B4DDV5, B4DR78, O00153, Q86VK4, Q9BQ19

UniProtKB/TrEMBL

B2RCP6, Q53FM1

Related

ENSP00000451763.2, ENST00000555044.6

Conserved Domains (4) summary

sd00017
Location:281 → 303

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:254 → 273

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:325 → 350

zf-H2C2_2; Zinc-finger double domain

pfam15909
Location:251 → 334

zf-C2H2_8; C2H2-type zinc ribbon

RNA

NR_040251.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (6) lacks an alternate exon and uses an alternate splice site in the 5' region, and also lacks an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AA652386, AC005480, AK298520

Related

ENST00000398139.7